Bookshelves emptied for no reason on Simple Touch 2?

So here's an update on what happened: Long story short, I had a few problems after messing with this whole situation as discussed in the comments, including microSD card damage. I erased and formatted both the SD card and the Nook. The update I had installed last night remained on the device. After that, I re-uploaded all of my books to the SD card with Calibre, added a few DRM-free books to a Bookshelf, and powered down the Nook. I then powered it back on. The DRM-free books were still on the Bookshelf after I restarted it.

Installing the update and erasing and formatting the Nook and microSD card also fixed the page number issue I mentioned with Mockingjay on the Home screen. No problems there.

Doing this wipe also allowed my DRM-free books to finally show up in the Library under the "All" selection.

tl;dr: I had to first install the latest update (1.1.2) and then wipe my Nook and microSD card for the 1.0.0 issues to be fixed. Moral of the story: Always update your device before using it!

I powered down my new Nook Simple Touch 2 after side loading some DRM-free books using Calibre. After I powered it back on, I found that the books that I had organized in bookshelves had disappeared, though they are still on my microSD card and readable.

Also, when reading a side loaded book, "Mockingjay," for example, the Home screen shows the page as 1/1 and returns you to page 1 should you tap that title, though entering the title from the top left-hand corner will take you to to the bookmarked page.

Any ideas as to why either of these events would happen? Thanks!